"Remaining 18 T1w scans (6.74%) demonstrated strong cerebral field of view cut offs disabling proper cerebral image analysis. Thus, these scans were rather excluded from the analysis."
René Labounek • 7:35 AM, Jul 15 (CDT): Make a new category in the exclude.yml file?
Rene Labounek • 8:42 AM, Jul 15 (CDT): I still think "brain_t1" category is needed, because csa_t1 lists you subjects where SC CSA measurement is impossible for some reasons (written as comment). But there are scans where you can measure SC CSA but not measure all cerebral volumes due to FOV cutting half of the brain. brain_t1 would list problematic subjects and comment can clarify the exact reason.
Julien Cohen-Adad • 9:02 AM, Jul 15 (CDT): ah! yes you are correct, i thought that 't1' was a category for the T1w scan, but it is not. Yes, you made a good point. Can you please open an issue and move the conversation we are currently having in the issue, so it is documented (and a subsequent PR will refer to that issue). thx!
TASKS
@mbondy023, please, can you send us list of the 18 problematic scans and descriptive reason why FS image analysis is imposible for these particular scans? + Are there any other scans where FS analysis will be imposible after the full done re-defacing? If you would keep text formating as in the exclude.yml file, it would be the best.
Then, @renelabounek or @mbondy023 can make a new branch, edit exclude.yml, submit PR and @jcohenadad or other admin accept the PR.
mbondy023
commented
2 years ago
FILE TO BE EXTENDED:
exclude.yml
BACKGROUND and CONVERSATION POINTING THE ISSUE
"Remaining 18 T1w scans (6.74%) demonstrated strong cerebral field of view cut offs disabling proper cerebral image analysis. Thus, these scans were rather excluded from the analysis."
René Labounek • 7:35 AM, Jul 15 (CDT): Make a new category in the exclude.yml file?
Julien Cohen-Adad • 8:31 AM, Jul 15 (CDT): no need for another category, a simple comment will do-- see example: https://github.com/spine-generic/data-multi-subject/blob/082dd0d7b5ad1eedf53ea9765910e2d68769d355/exclude.yml#L49
Rene Labounek • 8:42 AM, Jul 15 (CDT): I still think "brain_t1" category is needed, because csa_t1 lists you subjects where SC CSA measurement is impossible for some reasons (written as comment). But there are scans where you can measure SC CSA but not measure all cerebral volumes due to FOV cutting half of the brain. brain_t1 would list problematic subjects and comment can clarify the exact reason.
Julien Cohen-Adad • 9:02 AM, Jul 15 (CDT): ah! yes you are correct, i thought that 't1' was a category for the T1w scan, but it is not. Yes, you made a good point. Can you please open an issue and move the conversation we are currently having in the issue, so it is documented (and a subsequent PR will refer to that issue). thx!
TASKS
@mbondy023, please, can you send us list of the 18 problematic scans and descriptive reason why FS image analysis is imposible for these particular scans? + Are there any other scans where FS analysis will be imposible after the full done re-defacing? If you would keep text formating as in the exclude.yml file, it would be the best.
Then, @renelabounek or @mbondy023 can make a new branch, edit exclude.yml, submit PR and @jcohenadad or other admin accept the PR.
PREVIOUS ISSUE REPORTING BRAIN FOV PROBLEM
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